Use whatever app you're happy with and quick with until they shut down and then move on to the next app. The point of prototypes is speed and in getting an idea across. Not sure there is anything intrinsically more valuable in using one tool over another at this point in time.

I'm currently loving iA. Cross-platform sync through iCloud or Dropbox. Saves flat text files so you're never going to be stuck with notes in some weird app sync account if you find another alternative. It's also full Markdown, which I love.

I wish I could use Dropbox Paper, but I just can't seem to take notes in a browser on my laptop. It's strictly a personal thing that I have no real reason for.

I feel like I'm seeing too much of the "this process = better design results" these days. Just design how is most comfortable for you + what works best with your teams workflow. Maybe for a unique individual/team you could tweak a work flow or process, but the whole "this process is the best" stuff just drives me bonkers.